Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes.
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ABSTRACT:
SUBMITTER: Sahana S
PROVIDER: S-EPMC8216321 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Host genetic variants can determine their susceptibility to COVID-19 infection and severity as noted in a recent Genome-wide Association Study (GWAS). Given the prominent genetic differences in Indian sub-populations as well as differential prevalence of COVID-19, here, we compute genetic risk scores in diverse Indian sub-populations that may predict differences in the severity of COVID-19 outcomes. We utilized the top 100 most significantly associated single-nucleotide polymorphisms (SNPs) from a GWAS by Pairo-Castineira et al. determining the genetic susceptibility to severe COVID-19 infection, to compute population-wise polygenic risk scores (PRS) for populations represented in the Indian Genome Variation Consortium (IGVC) database. Using a generalized linear model accounting for confounding variables, we found that median PRS was significantly associated (p < 2 x 10−16) with COVID-19 mortality in each district corresponding to the population studied and had the largest effect on mortality (regression coefficient = 10.25). As a control we repeated our analysis on randomly selected 100 non-associated SNPs several times and did not find significant association. Therefore, we conclude that genetic susceptibility may play a major role in determining the differences in COVID-19 outcomes and mortality across the Indian sub-continent. We suggest that combining PRS with other observed risk-factors in a Bayesian framework may provide a better prediction model for ascertaining high COVID-19 risk groups and to design more effective public health resource allocation and vaccine distribution schemes.
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Project description:System-wide molecular characteristics of COVID-19, especially in those patients without comorbidities, have not been fully investigated. We compared extensive molecular profiles of blood samples from 231 COVID-19 patients, ranging from asymptomatic to critically ill, importantly excluding those with any comorbidities. Amongst the major findings, asymptomatic patients were characterized by highly activated anti-virus interferon, T/natural killer (NK) cell activation, and transcriptional upregulation of inflammatory cytokine mRNAs. However, given very abundant RNA binding proteins (RBPs), these cytokine mRNAs could be effectively destabilized hence preserving normal cytokine levels. In contrast, in critically ill patients, cytokine storm due to RBPs inhibition and tryptophan metabolites accumulation contributed to T/NK cell dysfunction. A machine-learning model was constructed which accurately stratified the COVID-19 severities based on their multi-omics features. Overall, our analysis provides insights into COVID-19 pathogenesis and identifies targets for intervening in treatment.
2021-03-12 | PXD024674 | Pride
Project description:A new global pandemic of coronavirus disease 2019 (COVID-19) has resulted in high mortality and morbidity. Currently numerous drugs are under expedited investigations without well-established safety or efficacy data. Pharmacogenomics may allow individualization of these drugs thereby improving efficacy and safety. In this review, we summarized the pharmacogenomic literature available for COVID-19 drug therapies including hydroxychloroquine, chloroquine, azithromycin, remdesivir, favipiravir, ribavirin, lopinavir/ritonavir, darunavir/cobicistat, interferon beta-1b, tocilizumab, ruxolitinib, baricitinib, and corticosteroids. We searched PubMed, reviewed the Pharmacogenomics Knowledgebase (PharmGKB®) website, Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines, the U.S. Food and Drug Administration (FDA) pharmacogenomics information in the product labeling, and the FDA pharmacogenomics association table. We found several drug-gene variant pairs that may alter the pharmacokinetics of hydroxychloroquine/chloroquine (CYP2C8, CYP2D6, SLCO1A2, and SLCO1B1); azithromycin (ABCB1); ribavirin (SLC29A1, SLC28A2, and SLC28A3); and lopinavir/ritonavir (SLCO1B1, ABCC2, CYP3A). We also identified other variants, that are associated with adverse effects, most notable in hydroxychloroquine/chloroquine (G6PD; hemolysis), ribavirin (ITPA; hemolysis), and interferon ? -1b (IRF6; liver toxicity). We also describe the complexity of the risk for QT prolongation in this setting because of additive effects of combining more than one QT-prolonging drug (i.e., hydroxychloroquine/chloroquine and azithromycin), increased concentrations of the drugs due to genetic variants, along with the risk of also combining therapy with potent inhibitors. In conclusion, although direct evidence in COVID-19 patients is lacking, we identified potential actionable genetic markers in COVID-19 therapies. Clinical studies in COVID-19 patients are deemed warranted to assess potential roles of these markers.
| S-EPMC7435176 | biostudies-literature
Project description:Vaccines against COVID-19 provide immunity to deter severe morbidities associated with the infection. However, it does not prevent infection altogether in all exposed individuals. Furthermore, emerging variants of SARS-CoV-2 impose a threat concerning the competency of the vaccines in combating the infection. This study aims to determine the variability in adverse events and the extent of breakthrough infections in the Indian population. A retrospective study was conducted using a pre-validated questionnaire encompassing social, demographic, general health, the status of SARS-CoV-2 infection, vaccination, associated adverse events, and breakthrough infections in the Indian population. Informed consent and ethical approval were obtained as per Indian Council of Medical Research (ICMR) guidelines. Participants, who provided the complete information, were Indian citizens, above 18 years, and if vaccinated, administered with either Covishield or Covaxin, were considered for the study. Data have been compiled in Microsoft Excel and analyzed for statistical differences using STATA 11. The responses from 2051 individuals fulfilling the inclusion criteria were analyzed. Among 2051, 1119 respondents were vaccinated and 932 respondents were non-vaccinated. Among 1119 vaccinated respondents, 7 were excluded because of missing data. Therefore, out of 1112 vaccinated, 413 experienced adverse events with a major fraction of younger individuals, age 18-40 years, getting affected (74.82%; 309/413). Furthermore, considerably more females than males encountered adverse consequences to vaccination (p < 0.05). Among vaccinated participants, breakthrough infections were observed in 7.91% (88/1112; 57.96% males and 42.04% females) with the older age group, 61 years and above (odds ratio, 3.25 [1.32-8.03]; p = 0.011), and males were found to be at higher risk. Further research is needed to find the age and sex-related factors in determining vaccine effectiveness and adverse events.
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Project description: Not available
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Project description:BackgroundPoor emotion regulation is associated with post-traumatic stress symptoms (PTSS). However, limited prospective research prevents any directional conclusions. No known studies have assessed emotion regulation with PTSS in American Indians, a high-risk population for poor mental health outcomes. The present prospective study explored whether emotion regulation strategies (cognitive reappraisal, expressive suppression) predicted later PTSS related to the COVID-19 global pandemic in a solely American Indian sample.MethodsAmerican Indian participants (N = 210; Mean (SD) age = 54.85(13.08) years, 58.7% female) completed the Emotion Regulation Questionnaire (ERQ) during Phase 1 (a few weeks before pandemic declaration) and the Impact of Event Scale-Revised (IES-R) with respect to the COVID-19 pandemic during Phase 2 (7-8 weeks after pandemic declaration). Bivariate correlations and hierarchical linear regression analyses were utilized.ResultsERQ reappraisal was negatively associated with IES-R total scores, such that higher reappraisal predicted lower PTSS. In contrast, ERQ suppression was positively associated with IES-R total scores, such that higher suppression predicted higher PTSS.ConclusionsGreater suppression and lower reappraisal predicts PTSS in response to the COVID-19 pandemic in an entirely American Indian sample, providing critical information for future interventions in a population at high-risk for mental health disparities.
| S-EPMC7870357 | biostudies-literature
Project description:The emerging infection of COVID-19 was initiated from Wuhan, China, have been spread to more than 210 countries around the globe including India. The clinical symptoms of COVID-19 are very similar to other respiratory viruses. The number of laboratory-confirmed cases and associated deaths are increasing regularly in various parts of the World. Seven coronaviruses (229E, NL63, OC43, HKU1, SARS, MERS and, COVID-19) can naturally infect human beings. Out of these four (229E-CoV, NL63-CoV, OC43-CoV, HKU1-CoV) are responsible for mild upper respiratory infections, while SARS-CoV, MERS-CoV, and COVID-19 are well known for their high mortality. Few mild strains of coronaviruses are circulating in India but there is no evidence of SARS and MERS outbreaks. The COVID-19 is an emerging viral infection responsible for pandemics. Fortunately, the mortality of COVID-19 is low as compared with SARS and MERS, the majority of its cases are recovered. The death toll of COVID-19 is high even after its low mortality because COVID-19 causes a pandemic while SARS-CoV and MERS-CoV cause epidemics only. COVID-19 influenced the large segments of the world population, which led to a public health emergency of international concern, putting all health organizations on high alert. COVID-19 is the first coronavirus after Spanish Flu 1918-1919, who has extremely influenced the health system, economy, and psychology of India. The present study review is on the general continent, virology, pathogenesis, global epidemiology, clinical presentation, diagnosis, treatment and control of COVID-19 with the reference to India.
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